Align Anthranilate synthase component 1 2; EC 4.1.3.27; Anthranilate synthase component I 2 (uncharacterized)
to candidate 209297 para-aminobenzoate synthase, component I
Query= curated2:Q9HS66 (488 letters) >MicrobesOnline__882:209297 Length = 334 Score = 169 bits (427), Expect = 2e-46 Identities = 113/293 (38%), Positives = 150/293 (51%), Gaps = 7/293 (2%) Query: 180 QSLAAAIRDGDPAVGPPPADSPAPFESVAGRAAFESRVRRIQDAIRDGDTFQANVSHRLD 239 + L+AA RDG A G A + + VR++ AIR GDT+Q N++ R Sbjct: 37 RGLSAAPRDGT-APGDDLALALDELVPSLDATTYPDGVRQVLAAIRRGDTYQLNLTSRFT 95 Query: 240 APAAVHPVAVFEA-LRDTNPAPYSGIVEFPGVDLVSASPELLLARRGRELTTEPIAGTR- 297 A A F L P P++ + ++S SPE L G E+ +PI GTR Sbjct: 96 ARRPGMDAAAFLLRLWQQRPTPFAAYLHAGRHRILSLSPERFLRVGGGEVLAQPIKGTRS 155 Query: 298 --PRGATPAEDDAARAALRADDKERAEHAMLVDLERNDLGKVSEYGSVAVPDYRRVDAYS 355 P +P E AALRAD KE AE +M+VDL RND+ Y SV VP + A Sbjct: 156 FDPATTSPGERARLEAALRADPKEHAELSMVVDLLRNDISATCAYDSVRVPRHCATFAVG 215 Query: 356 EVLHLVSEVTGRLRDSCSLRDAIAAVFPGGTITGAPKPRTMALIDTVEATRRGPYTGSLA 415 ++ + S+VTG LRD + D + FPGG++TG PKPRTM+LI+ +E R Y GSL Sbjct: 216 PLIQMCSDVTGTLRDGTTCLDLLRHAFPGGSVTGCPKPRTMSLIERIEPHPRDVYCGSLV 275 Query: 416 AIGFDGDATLSITIRTLVRRAAT--YHLRVGAGIVHDSTPAAEYDETLAKARA 466 A+ D SI IRT + T HL G+G+ DS P EY ET+ K A Sbjct: 276 AVAGPRDMDSSIAIRTAMYDTTTGLLHLYAGSGLTVDSDPEGEYRETVDKTSA 328 Lambda K H 0.317 0.135 0.397 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 530 Number of extensions: 36 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 488 Length of database: 334 Length adjustment: 31 Effective length of query: 457 Effective length of database: 303 Effective search space: 138471 Effective search space used: 138471 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory